rs3118526

Variant names:

• chr9-134445511-T-C
• rs3118526
• ENST00000745255.1:n.304T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-134445511-T-C
• chr9-134445511-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000745255.1(ENSG00000228877):​n.304T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,148 control chromosomes in the GnomAD database, including 60,922 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (60922 hom., cov: 30)
• Consequence: ENSG00000228877 ENST00000745255.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62
• Publications: 13 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745255.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228877	ENST00000745255.1		n.304T>C		non_coding_transcript_exon	Exon 1 of 6
	ENSG00000228877	ENST00000745258.1		n.309T>C		non_coding_transcript_exon	Exon 1 of 6
	ENSG00000228877	ENST00000745260.1		n.307T>C		non_coding_transcript_exon	Exon 1 of 7

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135716 AN: 152030 Hom.: 60878 Cov.: 30

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.857

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.893 AC: 135816 AN: 152148 Hom.: 60922 Cov.: 30 AF XY: 0.891 AC XY: 66214 AN XY: 74352

African (AFR) AF: 0.969 AC: 40217 AN: 41524

American (AMR) AF: 0.836 AC: 12759 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2922 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4253 AN: 5174

South Asian (SAS) AF: 0.713 AC: 3424 AN: 4804

European-Finnish (FIN) AF: 0.923 AC: 9768 AN: 10588

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59678 AN: 68004

Other (OTH) AF: 0.853 AC: 1799 AN: 2110

Alfa AF: 0.871 Hom.: 118303

Bravo AF: 0.890

Asia WGS AF: 0.787 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.10
PhyloP100		-3.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3118526; hg19: chr9-137337357; COSMIC: COSV62683941;